Contacts of the helix formed by residues 415 - 420 (chain F) in PDB entry 3HX0
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with CYS 415 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413F VAL* 3.6 16.2 - - - -
414F ALA* 1.3 72.8 - - - +
416F GLY* 1.3 73.7 + - - +
417F SER 3.6 0.2 + - - -
418F TYR* 3.2 11.3 + - - +
419F ARG* 3.2 17.9 + - - -
429F ASP* 2.7 22.0 + - - +
431F LEU* 3.8 15.5 - - - -
503F LEU* 3.8 25.1 - - - -
506F PHE* 3.4 37.9 - - + +
507F THR* 3.9 4.7 - - - +
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Residues in contact with GLY 416 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415F CYS* 1.3 84.3 - - - +
417F SER* 1.3 64.5 + - - -
418F TYR 2.9 0.2 + - - -
419F ARG* 3.1 7.3 + - - +
420F ARG* 3.2 22.1 + - - +
429F ASP* 3.5 8.2 + - - -
506F PHE 2.8 19.0 + - - -
507F THR* 3.8 6.6 - - - +
702F D3T 3.4 14.6 - - - -
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Residues in contact with SER 417 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386F ARG* 4.3 5.6 - - - -
415F CYS 3.6 0.2 + - - -
416F GLY* 1.3 71.1 - - - -
418F TYR* 1.3 66.4 + - - +
420F ARG* 3.2 17.9 + - - +
422F LYS* 3.2 44.8 + - - +
424F THR 4.3 0.2 - - - -
425F CYS* 3.4 18.2 - - - +
427F ASP 4.4 2.6 + - - -
702F D3T 2.7 46.0 + - - -
802F MG 4.5 0.2 - - - -
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Residues in contact with TYR 418 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389F ARG* 2.7 76.8 + - + +
392F ALA* 3.6 26.2 - - + -
393F THR* 3.0 30.6 + - - +
396F GLU* 5.3 5.9 + - + -
414F ALA* 3.3 34.8 - - + -
415F CYS 3.2 10.5 + - - +
416F GLY 2.9 0.8 + - - -
417F SER* 1.3 81.6 + - - +
419F ARG* 1.3 57.8 + - - +
421F GLY 2.8 9.4 + - - -
425F CYS* 3.8 9.6 - - - -
427F ASP 5.7 2.2 - - - +
428F VAL* 5.9 4.3 - - + -
429F ASP 5.9 1.3 - - - +
12Q G 3.0 39.0 + + + +
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Residues in contact with ARG 419 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389F ARG* 4.6 2.4 + - - +
413F VAL* 5.0 5.7 - - + +
414F ALA 3.3 20.2 - - - +
415F CYS* 3.2 13.0 + - - +
416F GLY 3.1 3.1 + - - +
418F TYR* 1.3 77.6 - - - +
420F ARG* 1.3 58.1 + - - +
421F GLY* 2.8 11.3 + - - -
503F LEU* 3.1 27.9 - - - +
507F THR* 2.6 44.7 + - + +
556F GLU* 2.6 41.3 + - - -
567F TYR* 4.4 4.2 + - - -
570F PRO* 3.8 28.6 - - + +
573F ARG* 4.0 0.2 - - - +
11Q T 5.8 2.1 - - - +
12Q G 4.4 20.4 + - - +
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Residues in contact with ARG 420 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416F GLY* 3.2 8.4 + - - +
417F SER* 3.6 18.1 - - - +
418F TYR 3.1 1.6 - - - -
419F ARG* 1.3 74.8 - - - +
421F GLY* 1.3 64.0 + - - +
422F LYS* 3.4 15.3 + - + +
507F THR* 2.8 45.1 + - + +
508F GLY* 4.0 2.8 - - - -
509F SER* 3.6 27.6 - - - +
570F PRO 3.4 25.8 - - - +
571F ALA* 3.8 20.4 - - - +
573F ARG* 3.8 12.3 - - - -
574F ASP* 2.7 32.1 + - - +
702F D3T 3.0 29.5 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il